RetrogeneDB ID: retro_cjac_2207

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:1074848..1075114(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: CPSF4L
• Ensembl ID: ENSCJAG00000019911
• Aliases: None
• Description: None

Sequence

>retro_cjac_2207
TTTGAAACAGACAATGAGATGCAAAAGGGCACTGGGCTCCCTTCTTTCCAGGGCATGGAGAAGTCGGACTCAGCTGTGTG
CAACTTCTTCACTAAAGGGCTCTGTGAGAAAGGGAAACTGTCCCTTCCCAGTATGACCGAGGGGACAAGATGGTGGTGTA
TAAGCACCAGCTCTGGGGGCTGTGCAACAGGGGCGACCACCATAAGTTCCTGCCTCAGTATGACCTCACCAGGATGCCCA
AGTGCTACTCCTACTGCAAGTTCGGT

Alignment

ORF - retro_cjac_2207 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.22 %
• Parental protein coverage: 53.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FETDVETQKGTGLLPFQGMDNEACPSCCLGPSALASPGKF-CPFWHDRGEKTVVCKHWLRGLCKKGDPCK
          FETD.E.QKGTGL..FQGM.......C......L...GK...P...DRG.K.VV.KH.L.GLC..GD..K
Retrocopy FETDNEMQKGTGLPSFQGMEKSDSAVCNFFTKGLCEKGKL<VPSQYDRGDKMVVYKHQLWGLCNRGDHHK

Parental  FLHQCDLTRRPECCFYSTFG
          FL.Q.DLTR.P.C..Y..FG
Retrocopy FLPQYDLTRMPKCYSYCKFG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.00 RPM	0.33 RPM
SRP051959_heart	0.00 RPM	0.42 RPM
SRP051959_kidney	0.00 RPM	0.40 RPM
SRP051959_liver	0.00 RPM	0.22 RPM
SRP051959_lung	0.00 RPM	0.42 RPM
SRP051959_lymph_node	0.00 RPM	0.48 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.35 RPM
SRP051959_spleen	0.00 RPM	0.44 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2207 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2207 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2207 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019911	1 retrocopy	retro_cjac_2207 ,
Myotis lucifugus	ENSMLUG00000009617	2 retrocopies	retro_mluc_1935, retro_mluc_1936,
Monodelphis domestica	ENSMODG00000025672	1 retrocopy	retro_mdom_558,